I have a design that uses 2 jumpered inputs for mode selection - the idea is that I turn on the internal pull-ups then selectively ground the inputs to give me a 4-way combo.

Laying out a PCB for it, the most convienient inputs would be 0 & 1 - but I was concerned since pin 1 is used as Tx output by the sketch loader, that when the programmed chip was in my PCB this pin will get set to output momentarily at some point, and therefore having it tied low would be bad....

Is that a correct assumption?

Ultimately the chip will be ISP programmed without the bootloader, but for now it's convenient to keep it in...

But if the bootloader is still in place (during my development/debug), does that not set the pin to output during it's "check if there's anything to upload" initialisation that happens before my code ever runs? :-/

Yes I was assuming that you were eliminating the boot loader. No problem though in place of a ground just put a 220R pull down resistor. That will look like a logic zero when the pin is an input and will limit the current to a safe value when it is an output.